SAXSdb — 1bo4

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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (SERRATIA MARCESCENS AMINOGLYCOSIDE-3-N-ACETYLTRANSFERASE)

Serratia marcescens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–168 Chain B； UniProt 1–168	Not recorded	SPD SPERMIDINE × 1 COA COENZYME A × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.8；277 K；SITTING DROP, 4 DEGREES C, 3.5MG/ML PROTEIN + 5MM COA, 100MM TRIS-HCL PH7.8, 0.8% PEG4K, 18% T-BUTANOL, 20MM SRCL2, 7% DIOXANE, 5% 2,4-METHYLPENTANEDIOL, 40MM HEXANEDIOL, 10MM DITHIOTHREITOL, 2MM TRIS(2-CARBOXY- ETHYL)PHOSPHINE-HCL, 10MM SPERMIDINE, 2.5% GLYCEROL, vapor diffusion - sitting drop, temperature 277K	Resolution 2.30 Å R-free 0.250

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1BO4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6BVC Crystal structure of AAC(3)-Ia in complex with coenzyme A Deposited 2017-12-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–177（177 aa）	Not recorded	COA COENZYME A × 2 CL CHLORIDE ION × 2 PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 4 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；0.2M NaCl, 25% PEG3350, 0.1M Na Citrate pH5.6, cryo paratone	Resolution 1.81 Å R-free 0.191

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q53396_SERMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–168； UniProt 1–168 Author chain B； PDBConstruct 1–168； UniProt 1–168

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bo4
Deposition date deposition_date	1998-08-08
Structure title title	CRYSTAL STRUCTURE OF A GCN5-RELATED N-ACETYLTRANSFERASE: SERRATIA MARESCENS AMINOGLYCOSIDE 3-N-ACETYLTRANSFERASE
Keywords keywords	;AMINOGLYCOSIDE 3-N-ACETYLTRANSFERASE, EUBACTERIAL AMINOGLYCOSIDE RESISTANCE, GCN5-RELATED N-ACETYLTRANSFERASE, COA-BINDING, TRANSFERASE ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.29 Å
Radius of gyration Rg (electron density) rg_electron	19.77 Å
Forward intensity I(0) i0	17883000.00
Molecular weight molecular_weight	31597.0 kDa
Excluded volume excluded_volume	39412 Å³
Envelope volume envelope_volume	46255 Å³
Hydration-shell volume shell_volume	19921 Å³
Envelope diameter envelope_diameter	75.0 Å
Shell Rg shell_rg	26.13 Å
Envelope Rg envelope_rg	20.10 Å
Shape Rg shape_rg	19.73 Å
Total Rg total_rg	20.80 Å
Total atoms total_atoms	2222
Residues n_residues	273
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	73.0 Å
Rg (real space) rg_real	21.28 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	1.7880e+07
I(0) uncertainty (real space) i0_real_error	2.4330e+05
Rg (reciprocal space) rg_reciprocal	21.28 Å
I(0) (reciprocal space) i0_reciprocal	17880000.0000
Solution quality estimate total_estimate	0.7767
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.371
Kurtosis Kurtosis kurtosis	-0.223
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3735000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.708; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PROTEIN (SERRATIA MARCESCENS AMINOGLYCOSIDE-3-N-ACETYLTRANSFERASE)
Molecular weight formula_weight	18488.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2475

MLRSSNDVTQQGSRPKTKLGGSSMGIIRTCRLGPDQVKSMRAALDLFGREFGDVATYSQHQPDSDYLGNLLRSKTFIALAAFDQEAVVGALAAYVLPKFEQPRSEIYIYDLAVSGEHRRQGIATALINLLKHEANALGAYVIYVQADYGDDPAVALYTKLGIREEVMH

来源 Source

来源生物 organism	Serratia marcescens
NCBI Class编号 ncbi_taxonomy_id	615
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SPERMIDINE
Molecular weight formula_weight	145.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	COENZYME A
Molecular weight formula_weight	767.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	253

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bo4a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.1 — N-acetyl transferase, NAT

Domain ID domain_id	d1bo4b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.1 — N-acetyl transferase, NAT

CATH v4.4 (2 domains)

Domain ID domain_id	1bo4A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	1bo4B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

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8. Citations (1)

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Unit-cell length a length_a	78.540 Å
Unit-cell length b length_b	102.260 Å
Unit-cell length c length_c	50.140 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.73 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2010
R_work r_work	0.2010
R_free r_free	0.2500

fit	/app/data/saxs_computation/bo/1bo4/1bo4.fit
pddf	/app/data/pr_computation/bo/1bo4/1bo4.pr.out
profile	/app/data/saxs_computation/bo/1bo4/1bo4.dat

CRYSTAL STRUCTURE OF A GCN5-RELATED N-ACETYLTRANSFERASE: SERRATIA MARESCENS AMINOGLYCOSIDE 3-N-ACETYLTRANSFERASE

1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (SERRATIA MARCESCENS AMINOGLYCOSIDE-3-N-ACETYLTRANSFERASE)

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction